[AMBER] clustering MD results

From: Jack Lee <jackk_lee.hotmail.com>
Date: Wed, 30 Mar 2011 16:34:06 +0800

Dear AMBER users,

I've tried to analyze MD results with clustering. I found manual of ptraj program with following example that produces 5 clusters using a RMS metric comparing the CA atoms:
  trajin traj.1.gz
  trajin traj.2.gz
  cluster out testcluster representative pdb \
  average pdb means clusters 5 rms .CA

Now, I won't specify the number of the clusters, but woule like to produce clusters based on the RMSD difference at cutoff = 2 angstrom.
How should I modify the script?

Thanks a lot for the help!

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Received on Wed Mar 30 2011 - 02:00:03 PDT
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